BN1848 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
WM 2.4143e-09 1.5992e-01
Layer 2 4.1266e-07 3.6175e-02
Layer 3 1.2799e-06 4.7612e-03
Layer 5 2.1127e-05 1.6833e-03
Layer 4 5.8890e-05 2.8039e-03
Layer 6 1.5782e-04 8.2547e-03
Layer 1 9.9409e-01 4.4709e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
UBQLN1 Expression Distribution
Gene Specificity Score (GSS)
UBQLN1 GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
UBQLN1 Layer 5 2.1543 0.6887
PCBP1 Layer 4 2.1152 0.6864
TRMT112 Layer 5 2.1152 0.6850
PGRMC1 Layer 5 2.2363 0.6794
OAT Layer 5 2.2227 0.6790
DDB1 Layer 4 2.0820 0.6770
MAPK8IP3 Layer 5 2.1484 0.6758
APLP2 Layer 5 2.3086 0.6748
SIRPA Layer 4 2.2227 0.6741
PSMC5 Layer 4 2.1250 0.6737
EIF4H Layer 5 2.2266 0.6737
HAGH Layer 5 2.0586 0.6723
PNPLA6 Layer 5 1.8926 0.6702
ATP8A1 Layer 5 1.9805 0.6695
ATP6V0B Layer 5 2.1016 0.6694
ELMO1 Layer 4 1.9990 0.6686
LAMTOR5 Layer 5 1.9189 0.6681
FLOT1 Layer 5 2.3398 0.6669
RAB2A Layer 5 2.1973 0.6664
STMN4 Layer 4 2.1250 0.6655
RANGAP1 Layer 4 2.1250 0.6652
FASN Layer 5 2.0254 0.6650
ATP6AP2 Layer 5 2.1777 0.6642
TMEM9 Layer 5 2.0449 0.6640
MAP4 Layer 5 2.1094 0.6639
DCTN2 Layer 5 2.1582 0.6638
NDUFS2 Layer 5 2.1914 0.6636
DDX6 Layer 5 2.0117 0.6630
PSMB4 Layer 5 2.1289 0.6628
TACC1 Layer 4 2.2969 0.6625
MRFAP1 Layer 5 2.1191 0.6625
MARCH6 Layer 5 2.1250 0.6624
HSPA9 Layer 5 1.9277 0.6623
HNRNPDL Layer 5 1.9580 0.6618
SQSTM1 Layer 5 2.1152 0.6611
DNAJC6 Layer 5 2.3867 0.6606
NFE2L1 Layer 5 2.2168 0.6606
VXN Layer 5 1.9629 0.6602
MAGED2 Layer 4 2.1973 0.6601
PPA1 Layer 5 2.1816 0.6598
PNKD Layer 5 2.0586 0.6595
MAPT Layer 5 2.1348 0.6594
ACTR2 Layer 5 2.1777 0.6591
CXXC5 Layer 4 1.8838 0.6586
TCEAL7 Layer 5 2.0957 0.6586
RNF10 Layer 4 1.9229 0.6584
PPP2CA Layer 3 2.0781 0.6583
SH3GLB2 Layer 5 2.0352 0.6583
MORF4L2 Layer 5 2.3086 0.6575
LGALS1 Layer 5 2.5215 0.6571

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1848
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1848_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1848/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1848/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1848/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1848/report/PD/BN1848_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1848/report/PD/BN1848_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 08:35:56
  • Number of Processes: 10
  • Spending Time: 0h 3m